intersectBed - multiple intersections

Question

[mbk0asis]

Hi, all!

I have two bed files to find common SNP's between them.

$ cat targets.bed
chr15   2462    2462    DNMT1-1
chr15   2463    2463    DNMT1-2

$ cat sample.33.bed
chr15   2461    2461    Idx.Pr.33
chr15   2462    2462    Idx.Pr.33

I expected the overlap at '2462'

chr15   2462    2462    DNMT1-1    chr15   2462    2462    Idx.Pr.33

instead I had three over laps

$ intersectBed -wa -wb -loj -a targets.bed -b sample.33.bed 
chr15   2462    2462    DNMT1-1 chr15   2461    2461    Idx.Pr.33
chr15   2462    2462    DNMT1-1 chr15   2462    2462    Idx.Pr.33
chr15   2463    2463    DNMT1-2 chr15   2462    2462    Idx.Pr.33

I think this reuslt was caused because the bedtools uses 0-based coordinate system.

How can I solve this problem?

Thank you!

[Alex Reynolds]

BED uses coordinates in a half-open interval, so if you are using a BED file to define the position of a base in a SNP, the start position should be one less than the stop position (or the stop position one more than the start, depending on your original coordinate system).

Answer 1

[Jeffin Rockey]

Just like you doubted, please make both the bed files in proper bed format and then do intersect. This link may help you with the co-ordinates systems. It has nice illustrations.

Still, the result would have non overlapping entry like below since -loj option is used

chr15   2461    2462    DNMT1-1 chr15   2461    2462    Idx.Pr.33
chr15   2462    2463    DNMT1-2 .       -1      -1              .

Answer 2

[sysbiocoder]

The following command report only those intersections where 100% of the query record is overlapped

bedtools intersect -wa -wb -a targets.bed -b sample.33.bed -sorted -f 1.0